Morales 2018, Plant Cell Environ.

The Morales 2018 model — "Dynamic modelling of limitations on improving leaf CO₂ assimilation under fluctuating irradiance" — extends the classical steady-state Farquhar-von Caemmerer-Berry framework into a fully dynamic description of C₃ photosynthesis, built to identify which regulatory processes limit carbon gain when irradiance fluctuates rather than staying constant. On top of the biochemical CO₂-fixation reactions (RuBP and PGA pools, Rubisco carboxylation/oxygenation, TPU and electron-transport limitations), it resolves the kinetics of the mechanisms that actually lag behind a change in light: energy-dependent non-photochemical quenching (qE) and its relaxation, photoinhibition and PSII repair, chloroplast movement (leaf absorptance), Rubisco activation state, and stomatal opening/closure. A four-compartment CO₂/H₂O diffusion pathway — ambient, boundary layer, substomatal and mesophyll/chloroplast — couples these regulatory dynamics back to the leaf gas-exchange measurements the model is validated against.

The model was parameterised and tested against combined gas-exchange and chlorophyll-fluorescence time courses recorded on Arabidopsis thaliana (Col-0) and a panel of mutants specifically impaired in Rubisco activation, qE or sucrose synthesis, which let the authors isolate the individual contribution of each kinetic limitation to the loss of carbon assimilation under fluctuating light. It predicted that the rate of Calvin-cycle enzyme activation and the rate of stomatal opening are the most limiting processes on their own (up to 17% each), with a combined improvement of up to 32% if all kinetic limitations were removed simultaneously — a result later used to guide breeding and engineering targets for photosynthetic efficiency under field-realistic, fluctuating light. It is included in GreenSloth as a detailed, experimentally validated dynamic gas-exchange model that links photoprotection, Rubisco regulation and stomatal behaviour within a single framework.

Model definition